Cut out shape in mesh without messing up the mesh completely!
You'll want to use custom normals. Blender has a data transfer modifier which allows you, among many other things, to copy normals from one mesh to another.




Keep your untouched mesh as the source for the normals and make a copy of it.
For the copy, add the boolean modifier or whatever you want to use to cut it.
On the copy, in the Data Tab, turn on Auto Smooth and click Add Custom Split Normals Data. We do that to allow the use of custom normals.
Add a Data Transfer modifier to the copy. Set the untouched source as the modifiers' Source Object. Turn on face corner data, and in the dropdown menu right to that, select Projected Face Interpolated.
Finally you can apply the data transfer modifier and delete the normals' source model.